Contacts of the helix formed by residues 102 - 115 (chain A) in PDB entry 4Y2P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 5.4 0.4 + - - -
13A VAL* 3.0 24.6 + - - +
14A LEU 2.7 19.1 + - - +
15A ALA* 4.2 1.8 - - - +
16A LEU* 3.6 27.4 - - + +
100A LYS 3.3 1.6 + - - -
101A ILE* 1.3 69.7 - - - +
103A ARG* 1.3 64.3 + - - +
104A PRO* 3.2 17.8 - - - +
105A MET* 3.0 15.9 + - - +
106A LEU* 3.0 20.3 + - - +
203A VAL* 6.0 0.2 - - - +
206A THR* 2.8 29.1 + - - +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.2 39.7 + - - +
102A ASN* 1.3 71.2 - - - +
104A PRO* 1.4 67.2 - - + +
105A MET 3.3 0.2 + - - -
106A LEU* 3.3 16.0 + - - +
107A GLN* 2.8 32.4 + - - +
142A GLU* 2.7 41.0 + - - -
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Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASN* 3.2 15.3 - - - +
103A ARG* 1.4 91.5 - - + +
105A MET* 1.3 55.8 + - - +
107A GLN* 3.4 15.2 + - + +
108A ALA* 3.1 26.2 + - - +
206A THR* 4.2 9.0 - - + -
207A ASP* 5.8 2.0 - - - +
210A LEU* 3.8 20.7 - - + +
221A LEU 5.7 0.3 - - - +
222A LEU* 5.8 2.2 - - + -
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Residues in contact with MET 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.9 26.4 - - + -
13A VAL* 3.6 32.3 - - + +
14A LEU* 3.7 15.9 - - + -
102A ASN* 3.0 27.9 + - - +
104A PRO* 1.3 76.0 - - - +
106A LEU* 1.3 67.8 + - - +
108A ALA* 3.3 6.1 + - - +
109A ALA* 3.0 21.1 + - - +
183A LEU* 4.4 5.4 - - - -
203A VAL* 4.2 19.5 - - + -
206A THR* 4.2 14.5 - - + +
209A ALA* 4.6 8.5 - - + -
210A LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.8 11.3 - - + +
101A ILE* 3.9 25.8 - - + -
102A ASN 3.0 11.5 + - - +
103A ARG* 3.6 24.5 - - - +
105A MET* 1.3 78.0 - - - +
107A GLN* 1.3 61.3 + - - +
109A ALA* 3.1 2.2 + - - +
110A LEU* 2.9 51.5 + - + +
142A GLU* 5.2 0.4 - - - +
143A LEU* 4.1 13.7 - - + -
146A HIS* 3.8 30.1 - - + +
147A PHE* 4.2 12.8 - - + -
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 2.8 20.0 + - - +
104A PRO* 3.9 13.7 - - + +
105A MET 3.2 0.2 - - - -
106A LEU* 1.3 73.7 - - - +
108A ALA* 1.4 59.8 + - - +
110A LEU* 3.4 14.4 - - + +
111A MET* 2.9 29.4 + - + +
221A LEU 5.1 7.4 - - - +
224A THR* 3.1 32.7 - - + +
225A PRO 4.1 4.5 - - - +
226A ALA* 5.9 0.4 - - - +
227A PRO* 4.2 29.3 - - + +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 5.3 0.2 - - + -
104A PRO 3.1 10.1 + - - +
105A MET* 3.6 9.0 - - - +
106A LEU 3.2 0.2 - - - -
107A GLN* 1.4 78.1 - - - +
109A ALA* 1.3 57.4 + - - +
111A MET* 3.2 3.0 + - - +
112A LEU* 2.9 34.3 + - - +
210A LEU* 3.6 30.3 - - + -
213A LEU* 4.4 5.6 - - + -
221A LEU* 3.8 29.7 - - + +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.8 25.7 - - + -
14A LEU* 4.9 0.2 - - + -
105A MET 3.0 11.7 + - - +
106A LEU* 3.1 8.0 + - + +
108A ALA* 1.3 75.4 - - - +
110A LEU* 1.3 58.8 + - + +
112A LEU* 3.3 5.0 + - - +
113A ARG* 2.8 30.9 + - - +
119A THR* 3.9 5.9 - - + +
146A HIS 5.6 1.3 - - - +
147A PHE* 3.6 36.8 - - + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 2.9 31.6 + - + +
107A GLN* 3.4 18.6 - - + +
109A ALA* 1.3 76.2 - - + +
111A MET* 1.3 56.9 + - - +
113A ARG* 3.2 8.5 + - + +
114A LYS* 2.7 30.7 + - - +
146A HIS* 3.2 56.8 - - + +
230A THR* 5.9 0.4 - - - +
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Residues in contact with MET 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN* 2.9 18.5 + - + +
108A ALA* 3.2 5.1 + - - +
110A LEU* 1.3 76.1 - - - +
112A LEU* 1.3 58.4 + - - +
114A LYS* 3.1 36.1 + - - +
115A LYS* 2.8 55.5 + - - +
219A ILE* 4.2 4.5 - - + -
220A GLN 3.9 10.1 - - - +
221A LEU* 3.6 24.7 - - + -
224A THR* 4.6 25.1 - - + +
225A PRO* 6.3 0.7 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 3.8 24.5 - - + -
8A PHE* 4.4 5.2 - - + -
108A ALA 2.9 18.8 + - - +
109A ALA* 3.7 4.0 - - - +
111A MET* 1.3 76.0 - - - +
113A ARG* 1.3 62.0 + - - +
115A LYS* 3.1 10.9 + - - +
116A GLY 3.3 0.5 + - - -
117A PHE* 2.9 42.0 + - + +
119A THR* 4.7 2.9 - - + -
213A LEU* 3.9 32.1 - - + -
217A THR* 4.0 17.5 - - + +
219A ILE* 3.7 26.0 - - + -
221A LEU* 3.9 16.6 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA 2.8 14.4 + - - +
110A LEU* 3.5 12.2 - - + +
112A LEU* 1.3 76.7 - - - +
114A LYS* 1.3 55.9 + - - +
116A GLY* 3.0 18.7 + - - -
117A PHE 3.7 14.7 + - - +
119A THR* 3.5 16.9 - - + +
145A MET 3.6 17.6 + - - -
146A HIS* 3.3 25.3 + - - +
147A PHE 3.6 11.5 + - - -
148A ASP* 2.7 50.9 + - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU 2.7 16.2 + - - +
111A MET* 3.3 41.9 - - - +
113A ARG* 1.3 73.3 - - - +
115A LYS* 1.3 60.4 + - + +
116A GLY 3.2 2.9 + - - -
227A PRO* 5.8 5.7 - - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A MET* 2.8 42.4 + - - +
112A LEU 3.1 6.1 + - - +
114A LYS* 1.3 75.0 - - + +
116A GLY* 1.3 59.5 + - - +
117A PHE* 3.7 5.8 + - - -
219A ILE* 3.8 43.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il